Storify/Tweet Notes from Noah Fierer’s talk at UC Davis

//[View the story “Noah Fierer talk at #UCDavis on biogeography of soil microbes” on Storify]

Noah Fierer talk at #UCDavis on biogeography of soil microbes

Storified by Jonathan Eisen· Thu, Jan 10 2013 22:44:52

At #UCDavis tomorrow: Noah Fierer @NoahFierer on “Exploring Terra Incognita: the biogeography of soil microorganisms” Eisen
Reminder – today 4 PM #UCDavis Seminar by Noah Fierer #microbes #microbiomes #biogeography #evolution #soil Eisen
Awaiting talk at #UCDavis by @NoahFierer- starting in a few minutes “Exploring terra incognita – the biogeography of soil microorganisms”Jonathan Eisen
Introduction for @NoahFierer talk at #ucdavis refers to him as a self described expert on cooties .. this has to be goodJonathan Eisen
@phylogenomics @noahfierer Did you ever play the Cooties game? I did, now I’m an entomologist. Trapped.Jack C. Schultz
For more on work of @noahfierer (whose talk at #UCDavis I am live tweeting) see Eisen
Now tweeting from @NoahFierer ‘s #UCDavis seminar “Exploring terra incognita: the biogeography of soil microorganisms” No eukaryotes tho :(Holly Bik
Fierer at #UCDavis defends referring to plants and animals as “macrobes” as better than calling small things microbesJonathan Eisen
Fierer at #UCDavis: 4000-2000 kg microbial biomass per hectare (from Fierer et al. 2009 Ecology letters)Jonathan Eisen
Fierer at #UCDavis: vast majority of soil microbial diversity undescribed, quotes Donald Rumsfeld as “patron saint of microbial ecology”Jonathan Eisen
Fierer at #UCDavis: example of Acidobacteria – up to 30% of bacteria in soil from this phylum yet only 5 described generalJonathan Eisen
Fierer at #UCDavis: using microbes to test principles of biogeography/ecology; using biogeography to learn about poorly understood microbesJonathan Eisen
Fierer at #UCDavis: in 2006 $10K = 400 bacteria IDd in each of 5 samples; 2012 $10K = > 10K bacteria IDd in each of 500 samplesJonathan Eisen
Fierer at #UCDavis: reduction in sequencing cost / increase in capacity allows 1st time biogeography studies of microbes on large scaleJonathan Eisen
Fierer: You can’t do ecology with 5 samples (old methods) – now costs have dropped, we can sequence 100s of samples to look at ecologyHolly Bik
Fierer at #UCDavis: dealing with this: “There is no biogeography of anything smaller than 1 millimeter” Bland Finlay Science 2005 vol 310Jonathan Eisen
Fierer at #UCDavis: collected soil samples from diverse biomes (tundra, desert, prairie, forest) & asked what calls “19th century” eco ??sJonathan Eisen
If the bacterial/archaeal people are doing 19th century ecology (as says @NoahFierer), then us eukaryote people are stuck in the dark ages..Holly Bik
Fierer at #UCDavis discussing Lauber et al. 2009 – ~1000 sequences per sample x 80 + samplesJonathan Eisen
Fierer at #UCDavis discussing this figure from 2009 paper – where simple ordination did not distinguish samples wellJonathan Eisen
Fierer at #UCDavis now discussing Figure B from saying that soil pH shows strong association w/ microbe Beta diversityJonathan Eisen
“@Dr_Bik: Fierer: You can’t do ecology with 5 samples costs have dropped, we can sequence 100s of samples 4 ecology” SORT OF. Whoo R U? $$$Jack C. Schultz
Fierer et al. refs from 2009 paper that shows good relationship between soil pH and alpha diversityJonathan Eisen
Fierer at #UCDavis: their soil data did not show any obvious relationship to latitude, mean annual temp, or other variables looked atJonathan Eisen
Fierer at #UCDavis: their data showing relationship between pH and microbial diversity could have been due to some feature related to pHJonathan Eisen
Fierer at #UCDavis: looked at soil microbes in one biome in arctic and still had correlation with pH and diversityJonathan Eisen
Fiere at #UCDavis: refs. where even in controlled system (Rothamsted Research) pH & microbial diversity correlatedJonathan Eisen
Does pH itself drive soil microbial assemblages, or aluminum toxicity (Al and pH closely linked)? We don’t know yet says @NoahFiererHolly Bik
At #UCDavis @NoahFierer: discussing PNAS 2012 Soil paper – metagenomics of VERY different soil samplesJonathan Eisen
At #UCDavis @NoahFierer: in soil metagenomic data only ~ 20% of reads could be annotated (i.e., function predicted)Jonathan Eisen
At #UCDavis @NoahFierer: in soil metagenomic data there is a weak ++ correlation between 16S PD and functional diversityJonathan Eisen
At #UCDavis @NoahFierer: desert soils VERY different from other soils in beta diversity of taxa & functionsJonathan Eisen
At #UCDavis @NoahFierer: looked are which genes were driving the major differences beta. soils in deserts & other locationsJonathan Eisen
At #UCDavis @NoahFierer quotes Willa Cather “elsewhere the sky is the roof of the world but here the earth was the floor of the sky”Jonathan Eisen
. @NoahFierer heads to 19th century graveyards to sample native prairie grass habitats for soil microbes. One of least disturbed sites..Holly Bik
At #UCDavis @NoahFierer refs paper that modelled distributions of Sasquatch Eisen
At #UCDavis @NoahFierer discussing collaborative work w/ Josh Ladau from UCSF (who I collaborate w/ too)Jonathan Eisen
At #UCDavis @NoahFierer says “Microbial ecology needs more Ecologists” (emphasizes the capital EJonathan Eisen
At #UCDavis @NoahFierer: Ecology needs more microbial ecologyJonathan Eisen
Pleas frm @NoahFierer: Microbial ecology needs more Ecologists–lots of data out there, not being fully used, & lots of reinvention of wheelHolly Bik
At #UCDavis @NoahFierer: ecological restoration projects need to consider microbes as part of the storyJonathan Eisen
@phylogenomics: @NoahFierer: ecological restoration projects need to consider microbes as part of the story” or quit stupid reconstructionJack C. Schultz
@phylogenomics: At #UCDavis @NoahFierer says “Microbial ecology needs more Ecologists” (emphasizes the capital E” ) Brilliant!Jack C. Schultz
@phylogenomics Lots of reasons reconstruction is purely subjective, starting with “which era do we reconstruct?”. Not “science”Jack C. Schultz
@phylogenomics For a different take (e.g., why is YOUR reconstruction THE reconstruction?) see C. Schultz
Both true! – MTs: “@phylogenomics: At #UCDavis @NoahFierer: Ecology needs more MICROBIAL ecology” &”Microbial ecology needs more Ecologists”Gavin Collins
@jackcschultz sure some restoration projects have issues but the “not science” accusation makes you sound sillyJonathan Eisen

Notes from talk by Stephen J. O’Brien at #UCDavis

Stephen O’ Brien talked at UC Davis a few days ago. I met with him in the afternoon before his talk. It was one of the more interesting discussions I have had in a long time. He has done some very interesting and important work (e.g., comparative genomics, HIV, feline evolution) though most of what we talked about was not work per se (e.g., we talked a lot about baseball and big cats since my kids are obsessed with big cats).

Anyway, below is a “Storification” of tweets from his talk. Best part – he signed a copy of his Tears of the Cheetah: The Genetic Secrets of Our Animal Ancestors book with a dedication to my kids.
//[View the story “Steven J. O’ Brien talk at #UCDavis on CCR5/HIV/AIDS” on Storify]

Steven J. O’ Brien talk at #UCDavis on CCR5/HIV/AIDS

Storified by Jonathan Eisen· Mon, Jan 07 2013 20:12:09

Today at #UCDavis Stephen O Brien on “Three Decades of Genomics and AIDS” Eisen
Can’t wait for talk at 4 PM today at #UCDavis Genome Ctr by Stephen O’Brien on “Three Decades of Genomics and AIDS” Eisen
@phylogenomics Wow! Interesting topic. Wish I was attending.Setor Amuzu
As an evolutionary biologist am jealous of name of Obrien’s “Theodosius Dobzhansky Center for Genome Bioinformatics” Eisen
@phylogenomics any podcasts available?Cuquis R
SJ Obrien – head of new Dobzhansky Inst – intro by Harris Lewin, discussing how Dobzhansky finished his career here at #UCDavis:Jonathan Eisen
Lewin point out that Steven O Brien has been called the Indiana Jones of Genomes (e.g.., ) #ucdavisJonathan Eisen
Lewin: Steven O’ Brien is also one of the coordinators of the genome 10K project #UCDavisJonathan Eisen
Steven O Brien launching into his talk at #ucdavis Eisen
O’Brien at #UCDavis: Giving props to T. Dobzhansky and his pioneering work on population geneticsJonathan Eisen
O’Brien at #UCDavis: discussing how population genetics help lead to many whole fields/areas incl. conservation genetics, DNA forensics, etcJonathan Eisen
Stephen J. O’Brien: is on Plagues and people Contagion Genomics & Beyond. 3 areas: Gene Discovery, Conservation Genetics, DNA forensicsDawei Lin
O’Brien at #UCDavis: began work on AIDS epidemic partly as model for way to connect human genetics and infectious diseaseJonathan Eisen
O’Brien at #UCDavis: close to 30 million people have died of AIDS and close to 30 million more are infected w/ HIV & disease still spreadingJonathan Eisen
@Curosik don’t think soJonathan Eisen
O’Brien at #UCDavis: heterogeneity in progression in HIV led him to try to use advances in human genetics to look for AIDS restrictive genesJonathan Eisen
SJO: Oct. 1996 AIDS quilt is a symbol of the pandemic disease with 40K Tabard Emblems on that day at the Capitol Hill.Dawei Lin
O’Brien at #UCDavis: early in AIDS epidemic got access to samples from different groups of people to test role of human genes in progressionJonathan Eisen
O’Brien at #UCDavis: looked for genetic variation in AIDS resistance, progression rate, outcomes, response to HAART therapyJonathan Eisen
O’Brien at #UCDavis: in 1996 5 groups discovered that CCR5 (a G coupled seven transmembrane receptor) was target of HIV for cell entryJonathan Eisen
O’Brien at #UCDavis: looked for CCR5 mutations in cohorts of patients w/ HIV & found that homozygous mutations were protectiveJonathan Eisen
SJO: CCR5 is the binding target for HIV. People with CCR5 delta with a 32 peptide deletions do not have HIV infections.Dawei Lin
O’Brien at #UCDavis: those people heterozygous for CCR5 deletions showed slower progression of HIV infectionJonathan Eisen
@phylogenomics would love to see the stats methods on thatLewis Lab
@Lewis_Lab seems to be relatively old data …Jonathan Eisen
Obrien at #UCDavis: many scientists occasionally like to do more than publish in a good journal, some would like to translate to bedsideJonathan Eisen
SJO: People study genes about infectious diseases should not stop at publishing on a good journal, should bring it to the bedside.Dawei Lin
Obrien at #UCDavis: re: delta32 mutation in CCR5 and modifies Dobzhansky “nothing in medicine makes sense except in light of evolution”Jonathan Eisen
Obrien at #UCDavis: discussing how frequency of CCR5 delta32 mutation has increased rapidly over time; suggest this is due to ++ selectionJonathan Eisen
@phylogenomics I’m not seeing any open access/open data reports.Lewis Lab
Obrien at #UCDavis: 20 mutations in CCR5 have been found outside of delta32 mutation; 18/20 are amino acid changing; suggests ++ selectionJonathan Eisen
SJO: 1/5 people now is CCR5 delta 32 carriers. There are 22 variants. 18 of them changes peptides.Dawei Lin
Obrien at #UCDavis: Suggests something influenced CCR5 mutations prior to AIDS epidemic (admits much of his theories on this controversial)Jonathan Eisen
OBrien at #UCDavis now reading from Tears of the Cheetah his book on genetics / genomicsJonathan Eisen
O’Brien at #UCDavis: suggests that bubonic plague may have influenced CCCR5 mutation frequencies over timeJonathan Eisen
O’Brien at #UCDavis: discussing plague epidemic in 1665 and 1666 (reading from his book)Jonathan Eisen
@phylogenomics that got me the statistical test I was looking for–thanks. I don’t find the article very intuitive, thoughLewis Lab
O’Brien at #UCDavis: discussing their estimates of the age of the CCR5 delta 32 mutations by looking at the size of the linkage groupJonathan Eisen
O’Brien at #UCDavis: estimates of the date of the origin of the spread of the CCR5 delta 32 mutation is correlated w/ plague epidemicJonathan Eisen
O’Brien at #UCDavis: many many waves of plague epidemics over time (though he notes many other possible epidemics also at same general time)Jonathan Eisen
@phylogenomics thanks. This is a good case study for the stats class.Lewis Lab
@phylogenomics O’Brien suggests that bubonic plague may have influenced CCCR5 mutation frequencies” No doubt a 1-2 insC mutation.Donald Atkinson
SJO: Conspiracy theories of black death cause CCR5 mutation hike, which mostly found in Caucasians.Dawei Lin
O’Brien at #UCDavis: refs a 2004 Nature study of mice w/ CCR5 delta 32 homozygous mutation; -/- have 90+% reduction in Y.pestis uptakeJonathan Eisen
O’Brien at #UCDavis: after 9/11 & anthrax attack collaborated w/ people to look at smallpox infection in CCR5 delta 32 mutant cellJonathan Eisen
“The O’Brien at #UCDavis” stream of tweets by @phylogenomics is fascinating. Must-read for biology folks.Rob Quarles
@phylogenomics What is his book? I show the PBS vid he was in few years ago to my molec epi class each year to discuss CCR5/plague/HIVTara C. Smith
O’Brien at #UCDavis: many other viruses have been screened for whether they make use of CCR5Jonathan Eisen
@phylogenomics thanks for tweets re O’Brien lecture. Say hi to Steve for me!Kathy Belov
Obrien at #UCDavis: delta 32 mutations in CCR5 may lead to higher risk to West Nile virus …Jonathan Eisen
SJO: people with homozygous CCR5 delta mutations are susceptible to West Nile virus, not HIV.Dawei Lin
Obrien at #UCDavis: looking back to 1996 b/c this is when HAART therapy for HIV was startedJonathan Eisen
Obrien at #UCDavis: showing slide from Tony Fauci of FDA Approved antiretroviral drugs; now many new drugs going after CCR5 interactionJonathan Eisen
@phylogenomics cool! I will order it.. Thanks for the link!Cuquis R
@phylogenomics thanks!Tara C. Smith
Obrien at #UCDavis: discussing “The Berlin Patient” (see; had AML; prognosis bad; bone marrow tplant from CCR5delta32Jonathan Eisen
OBrien at #UCDavis: 2008 Gero Hitter – the doctor for “The Berlin Patient” shows up at AIDS conference; news finally comes out in WSJ 2008Jonathan Eisen
Obrien at #UCDavis: here is the WSJ news story about The Berlin Patient Eisen
Obrien at #UCDavis: says the story of the Berlin patient is an anecdote; emphasizes it is one patient; need more information / data / casesJonathan Eisen
Obrien at #UCDavis: refs SciAm article where gene therapy for HIV patients reported; he’s skeptical about peer reviewJonathan Eisen
Obrien at #UCDavis: some researchers have been looking at how CCR5 might influence Graft Versus Host Disease (see Eisen
Obrien at #UCDavis refs new Nature paper showing CCR5 is a receptor for MRSA leukotoxin (see Eisen
@KathyBelov will do …Jonathan Eisen
SJO: Patients with bone marrow transplants with CCR5 negative genotypes remain HIV free without drug treatments. A potential breakthrough.Dawei Lin
Obrien at #UCDavis giving props to George W. Bush for PEPFAR program Eisen
Obrien at #UCDavis: OBrien ends his talk by thanking the patients who have provided samples cc: @rebeccasklootJonathan Eisen
Question at Obrien talk at #UCDavis: is CCR5 delta 32 the only restriction mutation? Obrien says yes but not yet translated to bedsideJonathan Eisen
Comment at talk by Obrien at #UCDavis: primate center at UCDavis played a major role in work on HIVJonathan Eisen
Comment at Obrien talk at #UCDavis: says to students in crowd that you have heard a talk about thinking which most people don’t do anymoreJonathan Eisen
@phylogenomics Nice. He definitely saw importance of donor appreciation/respect differently than most in the early days.Rebecca Skloot
@phylogenomics I wanna know what happened to his amazing frozen zoo at NCI! Hope he took it w/him; he worried re who would take care of itRebecca Skloot
@RebeccaSkloot he did not discuss this …Jonathan Eisen
Love @phylogenomics tweets on O’Brien’s talk at #UCDavis. Everything he said on CCR5/HIV/Berlin pt is right up my alley.Nathalia Holt
My kids are very happy w/ autographed copy of “Tears of the Cheetah” Steven O Brien gave me after his talk at #ucdavis Eisen
As follow up to post about “Tears of a cheetah” – my kids are a bit obsessed w/ big cats … Eisen
@phylogenomics How do the cats get along with all the microbes?Cindy Manson
@CynthiaManson1 extremely well Eisen

Thank you interwebs: help proving fungi are cool

Well, am teaching three lectures this week on Fungal Diversity for BIS002C at UC Davis. And I decided tonight to ask the internet for help finding cool new stories on fungi. And boy did the internet come through in the clutch. Thanks internet. See Storification of Twitter and Facebook discussions below:[View the story “Fungi are cool” on Storify]

Fungi are cool

Storified by Jonathan Eisen · Sun, Nov 04 2012 23:13:14

Twitter Discussion after I asked for suggestions …
Prepping 3 lectures on Fungal Diversity for Intro Bio class at #UCDavis – looking for suggestions for coolest recent fungal stories/studiesJonathan Eisen
@phylogenomics Saccharomyces eubayanus & the new world origin of lager yeast…jashapiro
@phylogenomics well, in the news, jump in fungi in metagenome studies in gulf post BP spill.Kenneth Bruno
@phylogenomics the obvious 1 is the fungal meningitis outbreakKitt Klaiss
@jashapiro reference?Jonathan Eisen
@phylogenomics This looks cool. I’m concerned that intro bio doesn’t have more micro, earlier. Is your syllabus available?Mark O. Martin
@KSBruno9 reference?Jonathan Eisen
@phylogenomics you can discuss Aspergillus around those iatrogenic fungal meningidites…Doctor_Strange
@phylogenomics And I love the whole story on fungi developing ability to degrade lignin leading to end of coal deposits.Kenneth Bruno
@phylogenomics I posted on FB, will get.Kenneth Bruno
@StrangeSource already on the listJonathan Eisen
Microbe domestication and the identification of the wild genetic stock of lager-brewing yeastAbstract Domestication of plants and animals promoted humanity’s transition from nomadic to sedentary lifestyles, demographic expansion, …
UW-Madison: University Communications: News PhotosPhotographs are available to media organizations and University of Wisconsin-Madison departments for news, editorial and public relations…
PLOS ONE: Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil SpillPLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific stud…
@phylogenomics I’m fond of Scott Strobel’s endophyte course and the discoveries they’re making w undergrads: Ory
Science Magazine lauds Yale science discovery courseAn innovative Yale science course that encourages undergraduates to discover and study plant-associated organisms has been recognized by …
@KSBruno9 heh – that is by @dr_bik … post doc in my lab …Jonathan Eisen
@phylogenomics @Dr_Bik cool, thought it was a great story. I’m from Louisiana so it was all close to home for me.Kenneth Bruno
@phylogenomics Hey, thank you! My students get taught (not by me) that bacteria are simple, don’t have cytoskeletons, no compartments, etc.Mark O. Martin
@phylogenomics @Dr_Bik Not to say that such a huge shift is necessarily a good thing…Kenneth Bruno
Biodiversity of FungiBiodiversity of Fungi is essential for anyone collecting and/or monitoring any fungi. Fascinating and beautiful, fungi are vital componen…
@phylogenomics Other thing that comes to mind is huge trend toward genome mining for secondary metabolites. Chemistry and genetics.Kenneth Bruno
World’s unique battle -Powerful Arthobortrys fungal adhesive employed to capture soil nematodenandkamat
World’s First video on soil nematode trapped by Drechslerella anchonia mycoadhesivenandkamat
@phylogenomics the responses u r getting is why twitter is cool now will spend part of today reading bout cool fungal researchSponch
May show this video by Louie Schwartzberg on fungi for #UCDavis class this week (although will probably use w/o sound)Jonathan Eisen
Fantastic Fungi: The Forbidden Fruitlouieschwartzberg
@Sponch2 ain’t that the truthJonathan Eisen
@phylogenomics Here is a paleontological fungal/liverwort controversy! O. Martin
A Strange Manuscript: When Giant Funguses Ruled the EarthAbout 400 million years ago, during the Devonian period, the world was a very strange place. Green plant life had begun to cover the land…
@phylogenomics Not totally fungal, but horizontal transfer of carotenoid production from fungi to aphids is cool.
Lateral transfer of genes from fungi underlies carot… [Science. 2010] – PubMed – NCBIPubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citation…
@jashapiro already on my list to cover .. I taught about this last few years …Jonathan Eisen
@phylogenomics Great story for a diversity course…jashapiro
Fermentation Guru Seeks Out New (and Old) Flavors”Oh, this is nice kimchi,” he said on a summer afternoon at Momofuku Noodle Bar, using chopsticks to pull crimson-coated knuckles of Napa…
@DrLabRatOry @phylogenomics I know the TAs of the class. Could get you in touch for skyping them in or send you pics from the field tripsDenina Hospodsky
Natural Products Version 2.0: Connecting Genes to Molecules – Journal of the American Chemical Society (ACS Publications)Abstract Natural products have played a prominent role in the history of organic chemistry, and they continue to be important as drugs, b…
Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms : Abstract : Nature Reviews MicrobiologyOne of the most promising applications of synthetic biology is the biosynthesis of new drugs from secondary metabolites. Here, we survey …
Fasebook Discussion after I asked for suggestions …
Prepping 3 lectures… | FacebookJonathan Eisen wrote: Prepping 3 lectures on Fungal Diversity… Join Facebook to connect with Jonathan Eisen and others you may know.
I would go for toe jam–that’s always popular.Amy Propps
well, I already talked about fecal transplants a few weeks ago … I think I am going to avoid the gross/semi gross this timeJonathan Eisen
Other than the contaminated steroids?Joanne Manaster
Ooo, that’s a good one!Amy Propps
New Ancient Fungus Finding Suggests World’s Forests Were Wiped Out In Global CatastropheTiny organisms that covered the planet more than 250 million years ago appear to be a species of ancient fungus that thrived in dead wood…
Joanne – will cover the steroids w/o a doubt .. but I want MORE …Jonathan Eisen
Tut Shares Tomb with Former Fungi: Scientific American PodcastBrown stains on the walls of Tut’s tomb are fungal mats, indicating a hurried burial. Cynthia Graber reports The tomb of King Tutenkhamen…
A lot of news coming out of the UK just now about threat to ash trees from Chalara: Saunders
ooh – King Tut fungus ..Jonathan Eisen
Chalara ash dieback outbreak: Q&AThe recent confirmed cases of Chalara ash dieback means it has become the latest threat to UK trees. Within the UK’s woodlands, ash is th…
That article looks like a stub, don’t know if there’s more to it.Amy Propps
Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen – Olson – 2012 – New Phytologist – Wiley Online Library
It’s hard to go past the Cordyceps “zombie fungus” 🙂 Video – and article – Saunders
4 New Species of Zombifying Ant Fungus Found | Wired Science | Wired.comSee Also: Citation: “Hidden diversity behind the Zombie-Ant fungus Ophiocordyceps unilateralis: Four new species described from Carpenter…
Cordyceps: attack of the killer fungi – Planet Earth Attenborough BBC wildlifebbcworldwide
Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical, Environmental, and Food MicrobiologistsSummary: Bacteria and fungi can form a range of physical associations that depend on various modes of molecular communication for their d…
I think mimicry examples are cool – fungus making a pheremone; Gibberellin, a plant hormone, is also produced by fusarium; Carrion smelling fungi attract flies to spread spores;Jason Stajich
Multitrophic interaction facilitates parasite-host relationship between an invasive beetle and the honey beeInternational Centre of Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya; ‡Institute of Food and Agricultural Sciences…
Plant Hormones GibberellinsGibberellins are diterpenes synthesized from acetyl CoA via the mevalonic acid pathway. They all have either 19 or 20 carbon units groupe…
“Mimicry in fungi” : Map of LifeMost of us are familiar with fungi in the form of mushrooms, some of which are brightly coloured and not likely to be mistaken for anythi…
Fungus + Virus = heat tolerance for thermophilic grasses and Stajich
Thermotolerance generated by plant/fungal symbiosis. [Science. 2002] – PubMed – NCBIPubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citation…
A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal ToleranceA mutualistic association between a fungal endophyte and a tropical panic grass allows both organisms to grow at high soil temperatures. …
It’s not new, but there’s a lot of good population biology/epidemiology on sudden oak death (Phytophthera ramorum)–especially the function of landscaping plants as vectors.If you want to use human health as a hook, you can’t go wrong with fungal sec…See MoreKen Callicott
Ken – phytophtera is not a fungus though …Jonathan Eisen
That’s right! I keep forgetting that work that showed them completely unrelated (well, you know what I mean) to the actual fungi–the curse of spending too much time around people who refer to them as water molds.Ken Callicott
look this video Jonathan Eisen….it’s amazing.. Gainza Cortes
BBC Planet Earth Cordyceps Fungus Finding of the holy mushroom – Diknek lorrie’sdnlscratcher
The deadly chytrid fungus: a story of an emergin… [PLoS Pathog. 2010] – PubMed – NCBIPubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citation…
underwater fruiting Psathyrella in Oregon discoved 3 years ago: Tighe
From a business side of things: 1) Using Oyster mushrooms to treat terrestial oil spills 2) BTTR in Emeryville that uses the left over coffee grounds to produce oyster mushrooms from whole foods etc 3) Eben Bayer’s TED talk on using mycellium to make packaging materials 4) Staments TED talk…fungus as pesticide replacement. 5) Cordyceps sinensis – Asia’s viagra, easily one of the most expensive mushrooms in the world and the hunt for them is causing major environmental problems in India the past summers.Damon Tighe
Eben Bayer: Are mushrooms the new plastic? | Video on TED.comTED Talks Product designer Eben Bayer reveals his recipe for a new, fungus- based packaging material that protects fragile stuff like fu…
Paul Stamets: 6 ways mushrooms can save the world | Video on TED.comTED
John Taylor’s recent reverse ecology study of NeurosporaMatthew Kane
Cambridge librarian finds forgotten fungus Charles Darwin brought back on the Beagle (and it was still wrapped in his newspaper)Fungi and seaweed collected by Charles Darwin on the Beagle Voyage has been uncovered wrapped in newspaper in a Cambridge University libr…
Also James Scott’s work on the angel’s share fungus and for the future lawyers in the room, what happens when fungal growth can be attributed to the distillers and thus they can be sued for this as …See MoreJason Stajich
The Mystery of the Canadian Whiskey Fungus | Wired Magazine | Wired.comThe air outside a distillery warehouse smells like witch hazel and spices, with notes of candied fruit and vanilla-warm and tangy- mellow…

Wanted – opinions/details on online systems for annotation of genomes and metagenomes

Doing a little survey/snooping around.  Trying to compile a list of available online tools for annotating microbial genomes and metagenomes.  And I am also trying to get comments on what people think of the various tools.  There are some obvious candidates to think about

But given that there are certainly many many more out there I decided to post a request to Twitter and Google plus and got some responses.

And from Google Plus where I asked “Researching blog post on free/online microbial genome/metagenome annotation services – looking for examples beyond IMG & RAST “:

Leaked insider docs from Heartland Institute goal: "dissuading teachers from teaching science" (ps hey Scholarly Kitchen do you support this?)

Yesterday I worried about the deceptive climate change related writings and work of one of the authors at the Scholarly Kitchen blog: Something rotten in the Scholarly Kitchen?
Basically, I wrote about how one of the authors at the Scholarly Kitchen – David Wojick – has been involved in some groups that have taken a decidedly deceptive anti-science stance on the issue of climate change.
I did not translate all of my worries into words because they were not completely formed. One of the reasons for my concern was the feeling that Wojick might be using his position in a apparently scholarly group to boost his authority in some way. Note – he has no apparent record of working on climate science yet he has written about it extensively with attempted authority.
Well, my unformed thoughts have hit me smack in the face today. Alexy Merz pointed me to this article published today:INTERNAL DOCUMENTS: The Secret, Corporate-Funded Plan To Teach Children That Climate Change Is A Hoax | ThinkProgress
The article quotes internal documents from the “Heartland Institute” discussing the development by one David Wojick of a “global warming curriculum for elementary schoolchildren that presents climate science as ‘a major scientific controversy.’ “
And more disturbing, the internal papers imply that they believe Wojick’s curricula have great potential for spreading because of his connections to organizations involved in “producing, certifying, and promoting scientific curricula.” So, in a way I think it is not a stretch to interpret his involvement in the Scholarly Kitchen as a way to boost his “authority” in academic circles even in the absence of any expertise in climate science.

And then as the evening progressed I found out more detail from the internal documents of the Heartland Institute that are even more disturbing:

Mind you, I generally try to avoid mixing writing about science and politics – and I am pretty open to diverse political points of view. But this is different.  The Heartland Institute and Wojick and others are using the same strategy used by Intelligent Design advocates. They want to “teach the controversy” and they want to make equivalent the thoughts of a few people with actual research by 1000s of scientists. I am all for freedom of speech and think anyone should be able to express their beliefs and opinions in a free and open manner.

The ultimate to me is in this leaked document:

Development of our “Global Warming Curriculum for K-12 Classrooms” project. Principals and teachers are heavily biased toward the alarmist perspective. To counter this we are considering launching an effort to develop alternative materials for K-12 classrooms. We are pursuing a proposal from Dr. David Wojick to produce a global warming curriculum for K-12 schools. Dr. Wojick is a consultant with the Office of Scientific and Technical Information at the U.S. Department of Energy in the area of information and communication science. His effort will focus on providing curriculum that shows that the topic of climate change is controversial and uncertain- two key points that are effective at dissuading teachers from teaching science. We tentatively plan to pay Dr. Wojick $100,000 for 20 modules in 2012, with funding pledged by the Anonymous Donor.

Let me repeat one part:

His effort will focus on providing curriculum that shows that the topic of climate change is controversial and uncertain – two key points that are effective at dissuading teachers from teaching science.[<a href=”” target=”_blank”>View the story “Scholarly Kitchen Bloggers response to questions” on Storify</a>]
UPDATE 4: More stories

UPDATE 5: 2-15 Kent Anderson, head of The Scholarly Kitchen blog responds and says actions of Wojick are irrelevant to his blog.
@phylogenomics @drs1969 it’s an irrelevant topic to this blog. It’s not a science blog, it’s a publishing blog.
Incredible. So – apparently being paid to deceive about the science behind studies of climate change is not relevant to a blog about publishing which has a big emphasis on peer review and science.

UPDATE 6: 2-15 8 PM More stories

UPDATE 7 with even more links:

Request for input – are there any rules regarding posting text of one’s own NSF (or other) grant proposals?

In response to a series of posts from Karen James (who is a biologist now in Maine and is director of the HMS Beagle Project) on Twitter, I am posting here to ask for input from the crowd.  On Twitter, Karen has been discussing her putting together an NSF proposal and was then celebrating a few days ago when it was done.

I have posted some of the twitter conversation below.  But to get directly to the point the question I have for everyone here is – are there any rules at the National Science Foundation that would prevent one from sharing with others a grant proposal that one has submitted?  Are there any rules against this at any agency?  I think there are none but apparently some are telling Karen otherwise.

Any information on this would be useful. Some of the twitter conversation is below:

So, @phylogenomics and others, with whom is it appropriate to share a submitted NSF proposal? Anyone? No one? Something in between?
1/12/12 6:15 PM

@kejames what do you mean by “appropriate”
1/12/12 6:15 PM

@kejames If I were you, I’d share the whole thing in public and make the reviews public as well. But I’m a minority view.
1/12/12 6:16 PM

@johnhawks Thanks, I’ve thought of that, actually. It is a federal agency after all. I’d need to redact confidential budget info, though.
1/12/12 6:18 PM

@kejames Yes, and possibly key personnel. My attitude is the success rate is so low, it can’t hurt and might draw visibility pre-review.
1/12/12 6:19 PM

@phylogenomics Best practice. My instinct is to share it with colleagues, collaborators and associates I think might be interested in it.
1/12/12 6:16 PM

@kejames what is the potential reason to not share?
1/12/12 6:17 PM

@phylogenomics That’s what I’m asking. Is there any rule or custom that prohibits sharing it far and wide?
1/12/12 6:19 PM

@kejames none that I know of – only reason not to is if you are worried about people “stealing” your ideas
1/12/12 6:19 PM

@phylogenomics Not worried about that in the slightest. If anything sharing it widely establishes it as “my” idea. Thanks.
1/12/12 6:20 PM

@johnhawks Or I could ask the key personnel if they’re okay w/ it. I think it would be nice to include them if they want to be included.
1/12/12 6:21 PM

@kejames I think Rosie Redfield posts hers on her blog
1/12/12 6:25 PM

@phylogenomics Thanks for that. I notice she just posts the project description itself, none of the other “stuff”and doesn’t list names.
1/12/12 6:28 PM

@kejames NSF proposals are your choice who to share with. Probably not best to post publicly, though.
1/12/12 6:25 PM

@DoctorZen Why not? As @phylogenomics notes, @RosieRedfield posts her grant proposals on her lab’s website:
1/12/12 6:29 PM

Anyone else besides @phylogenomics @doctorzen @johnhawks want to weigh in on how broadly I should share my just-submitted NSF proposal? 1/2
1/12/12 6:31 PM

@rdmpage @RosieRedfield @DoctorZen @johnhawks @phylogenomics @kzelnio So I asked the collaborators on the proposal. One replied… 1/2
1/13/12 4:50 AM

@rdmpage @RosieRedfield @DoctorZen @johnhawks @phylogenomics @kzelnio 2/2…”Sharing not wise! Could disqualify proposal.”
1/13/12 4:51 AM

.@kejames @rosieredfield @doctorzen @johnhawks @phylogenomics @kzelnio In other words fear of what grant agency will do trumps being open 😦
1/13/12 5:10 AM

@rdmpage I support being open; not sure every step always needs to be public. @kejames @rosieredfield @johnhawks @phylogenomics @kzelnio
1/13/12 5:18 AM

.@DoctorZen @kejames @rosieredfield @johnhawks @phylogenomics @kzelnio I agree, it’s not that it HAS to open, but that it COULD be
1/13/12 5:27 AM

@kejames @rdmpage @RosieRedfield @DoctorZen @johnhawks @kzelnio WTF? As far as I know there are NO NSF issues w/ sharing a proposal
1/13/12 7:00 AM

@kejames @rdmpage @RosieRedfield @DoctorZen @johnhawks @kzelnio Yes, need to discuss w/ collabs & get permission but not angst any rules
1/13/12 7:02 AM

@rdmpage @DoctorZen @kejames @rosieredfield @johnhawks @kzelnio agree w/ Rod – issue was whether it could be posted, not if it had to be
1/13/12 7:04 AM

@phylogenomics I’m following up w/ him to find out what he meant He’s a seasoned NSF grantee and reviewer. Have also contacted NSF directly.
1/13/12 7:08 AM

Wrap up of tweets from Joe Derisi talk

Just a quick post here – for those not following on Twitter – Joe Derisi gave a talk at UC Davis 1/9 and I posted some tweets about it.  Here they are:

Joe DeRisi getting ready for his talk at the #ucdavis Genome Center this am
1/9/12 9:57 AM
Joe Derisi’s first slide : “Bees, viruses, and plastids: a seminar in two parts” – I think he needs to work on his math
1/9/12 10:05 AM

DeRisi works with mobile honeybee colony trucks that travel around the country to service pollination needs
1/9/12 10:09 AM

DeRisi – one of the problems with figuring out what is causing CCD is we do not know much about “normal” healthy colonies
1/9/12 10:09 AM

Bee trucks start in Mississippi in winter, spring in Dakotas, then To california for almonds
1/9/12 10:10 AM
DeRisi got into bee studies because of colony collapse disorder CCD
1/9/12 10:13 AM

DeRisi – grinds up bees and then assays them with “bee pathogen chip” and sequencing
1/9/12 10:13 AM

Derisi discussing his new Plos one w/ SFSU paper showing phorid flies associated with bees
1/9/12 10:16 AM

Derisi says if you want your paper to get 1000s of hits you should mention Zombies somewhere as they did w/ “Zombie bees”
1/9/12 10:18 AM

Derisi: zombie bees are cool but the phorids are probably not associated with CCD
1/9/12 10:19 AM

DeRisi found six major pathogens associated w/ bees: Nosema, phorids, spiroplasma, notovirus, and others
1/9/12 10:22 AM

DeRisi – sequencing ground up bees – most reads are host or pathogens they know about – says key to characterizing new viruses is assembly
1/9/12 10:23 AM

DeRisi mentioning their PRICE assembler – an inductive assembly method
1/9/12 10:25 AM
@phylogenomics URL for PRICE is
1/9/12 10:30 AM

Why I love Joe Derisi “there will be a manuscript on the assembler someday… But the software is available for free now”
1/9/12 10:27 AM
DeRisi pooled together Bee samples prepped with various methods so that he could get diverse viruses covered
1/9/12 10:29 AM
DeRisi – lake sinai virus 2 is present in up to 10^11 copies per bee
1/9/12 10:35 AM

DeRisi – also present in bees – Crithidia – a trypanosome – related to known pathogens of other insects
1/9/12 10:36 AM

DeRisi – Crithidia also increases in abundance in winter
1/9/12 10:36 AM
DeRisi – sequenced and assembled genome of Crithidia – genome is interesting
1/9/12 10:37 AM
DeRisi – part two – the essential function of the Plasmodium apicoplast
1/9/12 10:38 AM

DeRisi – history of Studies of plasmodium apicoplast – organelle bound by four membranes – likely b/c result of secondary symbiosis
1/9/12 10:39 AM

Derisi discussing sequencing of apicoplast genome in 1990s by Gardner, McFadden, etc
1/9/12 10:40 AM

DeRisi – experiments suggest IPP is the sole essential product of apicoplast biology
1/9/12 10:47 AM

Charles Vest Seminar "The 21st century university: Purpose, problems & promise" wrap up

Here is a wrap up, via my twitter posts and responses to them, of the seminar yesterday by Charles M. Vest, ex head of MIT and current head of the National Academy of Engineering. I know it is a bit lazy not to rewrite a summary but I think the tweets do an OK job …

UPDATE – some new links regarding the talk

Here are my tweets:

Awaiting seminar by CHarles Vest, Pres. of US Natl. Acad. Engineering, past pres. of MIT #UCDavis
11/30/11 4:07 PM

Vest seminar “The 21st Century Research University Purpose, Problems and Promise” #UCDavis
11/30/11 4:08 PM
Charles Vest says Linda Katehi is an admired educational leader throughout the country #UCDavis
11/30/11 4:10 PM
Charles Vest: two main challenges for universities now are globalization and access (i.e., access to education)
11/30/11 4:13 PM
Charles Vest: currently trend to “brain interaction” across the globe, but need to work on how to connect people & computers better
11/30/11 4:14 PM
Vest: FoldIt tool is evidence for “collective intelligence” – the researchers involved weren’t just integrating computers but brains
11/30/11 4:15 PM
Vest discussing book A New Culture of Learning by Douglas Thomas and John Seely Brown “”
11/30/11 4:16 PM
Vest says location of universities still matter for many reasons incl. people need to be together and universities are embedded in cultures
11/30/11 4:17 PM
Vest: purpose of research universities is “to create opportunity” (1) for graduates, (2) for business/industry (3) nations/regions
11/30/11 4:19 PM
Vest: though research universities have many purposes, must be patient b/c hard to predict when benefits will occur
11/30/11 4:20 PM
Vest: MIT and Stanford work very well b/c research is side by side w/ applications
11/30/11 4:21 PM
Vest: few people understand that research universities are central to innovation (e.g., computing, laser, internet, gennomics)
11/30/11 4:22 PM
Note – I might disagree with Vest’s claim that Universities drove genomic innovation
11/30/11 4:23 PM
Vest: virtually every job in America depends on one or more university based innovations
11/30/11 4:23 PM
Vest six lessons including (1) teaching and research must be intimately intertwined and are inseparable
11/30/11 4:24 PM
Vest lesson 2: quality of research university is determined by quality of its faculty
11/30/11 4:25 PM

@phylogenomics I’ve quit telling kids to interview the faculty when applying to colleges. Parents don’t get it either. Ah, well.
11/30/11 4:29 PM

@oldivory good idea …
11/30/11 4:30 PM
Vest: need in particular young faculty to grow up through rising w/in university
11/30/11 4:26 PM
Vest lesson 3: science can flourish only in an open environment #herehere
11/30/11 4:26 PM
Vest lesson 4: young faculty must be free to study and teach what they believe is important (e.g., should not be assistants to Sr. faculty)
11/30/11 4:27 PM

@phylogenomics so not the European model.
11/30/11 5:11 PM
Vest lesson 5: competition engenders excellence in universities (drives improvement in research, teaching, ideas, facilities, etc)
11/30/11 4:28 PM

@phylogenomics @carloshotta Mild competition. Wild competition could lead to cheating, forgery, distrust, sabotage…
11/30/11 4:32 PM

@rmtakata @carloshotta he did not say it was perfect, just that it can be useful
11/30/11 4:34 PM
Vest Lesson 6: fundamental scholarship and research must be equal w/ applied research and innovation
11/30/11 4:29 PM
Vest: there is a danger in focus on applied issues that we ignore search for truth – must not be too utilitarian
11/30/11 4:30 PM

Vest says “never in his lifetime has it been so hard to hang onto his optimism” b/c Washington is broken
11/30/11 4:32 PM

As a young researcher, this concerns me RT @phylogenomics Vest says “never in his lifetime has it been so har… (cont)
11/30/11 5:23 PM
Vest: v. concerned w/ financial pressures on universities especially as it affects access & this started even before recent financial issues
11/30/11 4:33 PM
Vest: in the last decade real per student state appropriations have dropped >20% while costs have risen
11/30/11 4:35 PM
Vest: response to financial issues will be cut back on low demand classes, fewer low/middle $$ students, decr. in merit based aid & all bad
11/30/11 4:36 PM
Vest: the favorite solution to State university financial problems is to seek out of state students; this spirals out of control
11/30/11 4:37 PM
Vest: cites U. Michigan slogan from 19th century “an uncommon education for the common man”
11/30/11 4:37 PM

nice… but also woman? RT @phylogenomics: Vest: cites U. Michigan slogan from 19th century “an uncommon education for the common man”
11/30/11 4:43 PM

@jim_croft I was not endorsing – just reporting
11/30/11 4:44 PM

@phylogenomics of course – the sentiment is perfect, the wording is excellent, for its time, just a little dated in some circles today.
11/30/11 4:49 PM
Vest references Vannevar Bush’s vision “Science The Endless Frontier” for research & for access
11/30/11 4:39 PM
Vest references Vannevar Bush Quote on education access
11/30/11 4:42 PM
Vest: we must be good citizens of the world and contribute to and learn from increasing globalization of education
11/30/11 4:43 PM
Vest: all regions of the world are more/more linked/integrated w/ shared environment, challenges, resources, knowledge, humanity
11/30/11 4:45 PM
Vest: modern research universities concept was developed from Humboldt University in Germany in 1800s -> JHU in US -> others in US -> global
11/30/11 4:46 PM
Vest says he has a hard time contemplating scale of educational expansion in China and India
11/30/11 4:46 PM
Vest: the Yin and Yang of Universities are Competition and Collaboration
11/30/11 4:47 PM
Vest: people everywhere need opportunity from universities and thus MIT developed “Open Courseware” for anyone to use anywhere/anytime
11/30/11 4:48 PM

Vest: Open Courseware movement has spread globally – and it (and related initiatives) are a revolution
11/30/11 4:49 PM

@phylogenomics I’ve taken free courses from Stanford and MIT that imwoudlnt have been able to back in the day. Love open source education
11/30/11 5:07 PM

@phylogenomics my favorite was Robert sapolsky’s behavioral biology course from Stanford
11/30/11 5:08 PM
Vest: openness is the true spirit of education, democratization and empowerment
11/30/11 4:49 PM
Vest refs: “Unlocking the Gates” and “Abelard to Apple” – books about open education
11/30/11 4:50 PM
Vest: in 21st century we are observing the early emergence of a “Meta University” via open materials and platforms
11/30/11 4:51 PM
Vest: must rekindle spirit of research university as provider of opportunity while also promoting openness
11/30/11 4:52 PM
Here is more form Charles Vest on the “meta university”
11/30/11 4:53 PM
Vest: analog of Tip ONeil’s “all politics is local” need outreach to get people locally to understand importance of research universities
11/30/11 5:03 PM
Questioner asks Vest how to best export notion of democracy/ access
11/30/11 5:09 PM
Vest in response to question expresses dismay at how anyone could support the “Dream Act”
11/30/11 5:09 PM


@phylogenomics Dismay that anyone would *support* the DREAM Act? Why?
11/30/11 5:12 PM

@lukedones do you mean why would anyone be dismayed that some support the act?
11/30/11 5:15 PM

@phylogenomics Yes. Just wondering whether he gave a reason.
11/30/11 5:21 PM

@lukedones not that I remember
11/30/11 5:21 PM

@lukedones sorry – in looking at the Dream Act I am wondering if he misspoke and meant he supported it … no longer sure what he said
11/30/11 6:24 PM

@phylogenomics why no support for Dream Act?
11/30/11 7:01 PM

Sorry all; MAJOR error tweeting Charles Vest talk; I wrote he was against Dream Act; I think he/I got that backwards & must be for it
11/30/11 7:19 PM

@VoteBothell sorry – I think he must be for it – so either he or I got it backwards
11/30/11 7:20 PM

@phylogenomics Great, got it. Enjoy your tweets. I’ve been following you since the pepper spray. My support and thoughts are with UC Davis.
11/30/11 7:22 PM
@phylogenomics Thanks – I expected an academic would be for the Dream Act.
11/30/11 7:26 PM
Vest: we need more experimentation with how research is funded to try to find other ways
11/30/11 5:21 PM
Vest: should keep systems at basic science agencies but should try new approaches like ARPA-E
11/30/11 5:22 PM
Vest views Open Courseware as a new form of publication not really as “classes” per se, b/c not interactive
11/30/11 5:25 PM

Town Hall #2 – Chancellor Katehi meets w/ Faculty/Staff; Katehi receives much support

Quick post regarding the Town Hall meeting at UC Davis between the administration and faculty and staff.  I am going to tell it through pictures and twitter posts (mostly mine, with a few responses).  Will really try to write up a more essayish post ASAP.  I tried to match pictures to comments but some may be mismatched – please forgive me.  
If you want the punch line – it is pretty simple – lots and lots of support for Chancellor Katehi from faculty at staff with a few dissenting points of view.  Very few argued for the need for resignation (I think Nathan Brown was the only one but I may be wrong – Josh Clover and possibly others may have also said something along these lines).  And most said something positive about Katehi although most of the positive things were about how good a Chancellor people think she has been not about her handling of this incident and its aftermath.  Anyway – here are some pics and tweets … Also note I tried to record a few videos here and there and for some reason the only two that came out well were of two of the biggest critics of Katehi – Clover and Brown.  I am including those vids though if you only look at the vids you will get a mistaken impression regarding the amount of criticism vs. support for Katehi. 
Once again – banners are not allowed.  WTF?
The Tree of Life: Faculty and staff arriving for Town Hall meeting with Chamcellor
11/29/11 4:09 PM

@phylogenomics Why is the sign partially covered?
11/29/11 4:34 PM
People getting lottery numbers to speak

Gratuitous extra picture

Chancellor Katehi is now giving an opening mini statement to Town Hall #OccuppyUCDavis
11/29/11 4:11 PM

Katehi is saying that this has been a very very difficult 10 days #ucdavis
11/29/11 4:12 PM

Katehi also says there has been a lot of misinformation out there #ucdavis #OccuppyUCDavis
11/29/11 4:14 PM
@phylogenomics For Katehi to decry “misinformation” when she’s been its biggest purveyor with regard to #OccupyUCDavis is rich. #OWS
11/29/11 6:31 PM